Since eix-test-obsolete was mentioned here, apart from eix itself, I thought I'd write a recommendation. This is the only way I sync my portage nowadays: It performs a sync, updates the eix database and prints out a diff all in one go. I recommend invoking it as eix-sync -C '-q', which suppresses the typically verbose output of emerge --sync.

Package: app-portage/eix, of course :)

q, together with its plugins such as quse, qlop or qsize

Very useful set of portage-related functions, that can give similar information to equery and more. Part of app-portage/portage-utils.

quickpkg

A part of the core sys-apps/portage. Very helpful for building a tarball from an installed package if you want to temporarily downgrade/upgrade it for testing purposes. You get back to the packaged version using the -K (capital "K") switch to emerge. Tip: use quickpackage --include-config=y to include current configuration files in the package.

demerge

Lets you save the current list of installed packages in case you'd later want to revert. Kind of a "system checkpointing" tool.

The portage-utils suite with the q tool and it's many aliases. It gives you much information on things like which files are in a package, what use flags are used, their descriptions and much more. Quite indispensible.

For configuration file updating, my tool of choice is dispatch-conf, which is part of the standard portage install and saves a lot of work updating unchanged config files compared to etc-update.

It's been a while since I stopped using Gentoo, but apart from all the utilities
already suggested I used to like localepurge. It basically frees up disk space on the system by deleting unnecessary locale files and man pages.